Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters

Stigmas of holoparasitic Phelipanche arenaria (Orobanchaceae) - a suitable ephemeric flower habitat for development unique microbiome

BACKGROUND

Microbial communities have occasionally been observed in part of the ephemeric reproductive structure of floral stigmas, but their prevalence, phylogenetic diversity and ecological roles are understudied. This report describes the first study of bacterial and fungal communities in immature and mature stigma tissue of the endangered holoparasitic plant Phelipanche arenaria. Culture-dependent methods coupled with next-generation sequencing indicated that a small surface of the flower stigma was an unexpectedly rich and diverse microhabitat for colonization of microbial. We also compared the enzymatic activity of the bacterial communities between immature and mature stigmas samples.

RESULTS

Using high-throughput sequencing methods, we identified and classified 39 to over 51 OTUs per sample for bacterial OTUs represented by Pantoea agglomerans and P. ananatis, comprising 50.6%, followed by Pseudomonas, Luteibacter spp., Sphingomonas spp. with 17% of total frequency. The bacterial profile of immature stigmas of P. arenaria contained unique microorganisms (21 of the most numerous OTUs) that were not confirmed in mature stigmas. However, the enzymatic activity of bacteria in mature stigmas of P. arenaria showed more activity than observed in immature stigmas. In the fungal profile, we recorded even 80 OTUs in mature stigmas, consisting of Capnodiales 45.03% of the total abundance with 28.27% of frequency was created by Alternaria eichhorniae (10.55%), Mycosphaerella tassiana (9.69%), and Aureobasidium pullulans (8.03%). Additionally, numerous putative plant growth-promoting bacteria, fungal pathogens and pathogen-antagonistic yeasts were also detected.

CONCLUSIONS

Our study uncovered that P. arenaria stigmas host diverse bacterial and fungal communities. These microorganisms are well known and have been described as beneficial for biotechnological and environmental applications (e.g., production of different enzymes and antimicrobial compounds). This research provided valuable insight into the parasitic plant-microbe interactions.

A novel integrated industrial-scale biological reactor for odor control in a sewage sludge composting facility: Performance, pollutant transformation, and bioaerosol emission mechanism

In order to remove multiple pollutants in the sewage sludge (SS) composting facility, a novel integrated industrial-scale biological reactor based on biological trickling filtration and fungal biological filtration (BTF-FBF) was developed. This study examined bioaerosol emission, odour removal, pollutant transformation mechanism, and project investment. At an inlet flow rate of 7200 m³/h, the average removal efficiencies of hydrogen sulfide (H₂S), ammonia (NH₃), and volatile organic compounds (VOCs) during the steady stage were 97.2 %, 98.9 %, and 92.2 %. The BTF-FBF separates microbial phases (bacteria and fungi) of different modules. BTF removed most hydrophilic compounds, while FBF removed hydrophobic ones. Moreover, the reactor could effectively remove pathogens or opportunistic pathogens bioaerosols, such as Escherichia coli (61.9%), Salmonella sp. (85%), and Aspergillus fumigatus (82.1%). The pollutant transformation mechanism of BTF-FBF was proposed. BTF-FBF annualized costs were 324,783 CNY/year at 15 years. In conclusion, BTF-FBF provides new insights into composting facility bioaerosol, odour, and pathogen emission control.

Optimization of acrylic-styrene latex-based biofilms as a platform for biological indoor air treatment

Biotechnologies have emerged as a promising solution for indoor air purification with the potential to overcome the inherent limitations of indoor air treatment. These limitations include the low concentrations and variability of pollutants and mass-transfer problems caused by pollutant hydrophobicity. A new latex-based biocoating was herein optimized for the abatement of the volatile organic compounds (VOCs) toluene, trichloroethylene, n-hexane, and α-pinene using acclimated activated sludge dominated by members of the phylum Patescibacteria. The influence of the water content, the presence of water absorbing compounds, the latex pretreatment, the biomass concentration, and the pollutant load was tested on VOC removal efficiency (RE) by varying the formulation of the mixtures. Overall, hexane and trichloroethylene removal was low (<30%), while high REs (>90%) were consistently recorded for toluene and pinene. The assays demonstrated the benefits of operating at high water content in the biocoating, either by including mineral medium or water absorbing compounds in the latex-biomass mixtures. The performance of the latex-based biocoating was likely limited by VOC mass-transfer rather than by biomass concentration in the biocoating. The latex-based biocoating supported a superior toluene and pinene removal than biomass in suspension when VOC loading rate was increased by a factor of 4.

Treatment of gaseous emissions from tire manufacturing industry using lab-scale biofiltration pilot units

Continuously seeking the improvement of environmental protection, the limitation of exhaust emissions is of significance for the tire manufacturing industry. The aim of this study is to assess the potential of biofiltration for the treatment of such gaseous emissions. This work highlights that biofiltration is able to remove both hydrophilic and hydrophobic compounds within a single pilot unit of biofiltration. Due to Ethanol/Alkanes ratios (95/5 and 80/20), high performance levels were observed for low EBRT (16 and 12 s). After twenty days of stable running, the dynamic of stratification patterns could be explained as a result of species coexistence mechanisms. While its impact on performance has not been observed under stable operating conditions, the use of an adsorbent support such as granular activated carbon (GAC) could be relevant to promote system stability in the face of further perturbations, such as transient regimes, that are problematic in full-scale industrial applications.

Evaluation of NOx removal from flue gas and Fe(II)EDTA regeneration using a novel BTF-ABR integrated system

A promising process is under development for the removal of NOx and regeneration of Fe(II)EDTA in a novel biotrickling filter-anaerobic baffled reactor (BTF-ABR) integrated system at 50 ± 0.5 ℃. In this work, we investigated the NOx removal capacity of a BTF under different O₂ concentrations (7.0 vol%, 5.25 vol% and 3.5 vol%), and tested the effect of an ABR on NOx removal and regeneration of Fe(II)EDTA. The results showed that the NOx removal capacity was significantly increased with the O₂ concentration reduced from 7.0% to 3.5%. The microoxygen environment produced by the BTF-ABR integrated system was more conducive to the removal of NOx and regeneration of Fe(II)EDTA compared with that in the BTF. Real-time polymerase chain reaction (PCR) analysis showed that the coordinated expression of denitrification genes was the major reason for no N₂O emission, along with no nitrate and nitrite accumulation. The 16S rRNA gene amplicon sequencing analysis showed that the cooperation of denitrifying bacteria (Klebsiella, Petrimonas, Rhodococcus and Ochrobactium) and iron-reducing bacteria (Klebsiella, Geobacter and Petrimonas) in the system was the key to the stable and efficient removal of NOx and the regeneration of Fe(II)EDTA simultaneously.

Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

Effects of substrate fluctuation on the performance, microbial community and metabolic function of a biofilter for gaseous dichloromethane treatment

Dichloromethane (DCM) is a harmful volatile organic compound that usually originates from pharmaceutical industry. In this study, the treatment of gaseous DCM in a biofilter was investigated by gradually increasing the DCM inlet concentration. Nearly 80% of DCM could be removed when the inlet concentration was lower than 0.30 g m^-3. The maximum elimination capacity of 26.6 g m^-3·h^-1 was achieved at an inlet loading rate of 38.4 g m^-3·h^-1. However, with the increase in the inlet concentration to more than 0.60 g m^-3, the removal efficiency obviously decreased to about 40%. After a starvation period of 2 weeks, the biofilter rapidly recovered its performance. The Haldane model including a substrate inhibition term was applied to describe the kinetics of the biofilter. High-throughput sequencing indicated that DCM-degrading genera, such as Rhodanobacter sp., Hyphomicrobium sp., Rhizomicrobium sp., Bacillus sp., Pseudomonas sp., and Clostridium sp., were dominant in the biofilter in different operation phases. The microbial communities and diversities were greatly affected by the DCM concentration. Microbial metabolic functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results indicated that xenobiotics biodegradation and metabolism, carbohydrate metabolism, and amino acid metabolism were the three most abundant metabolic pathways of the microbes. The abundances of these metabolic functions were also altered by the DCM concentration.

Insight into the influence of microbial aggregate types on nitrogen removal performance and microbial community in the anammox process - A review and meta-analysis

The anaerobic ammonium oxidation (anammox) process has been paid close attention in the wastewater treatment field because of its energy-saving advantages. Different microbial aggregates have been used in the anammox process, and there is an urgent need to evaluate the comparative efficiencies of the widely used types of microbial aggregates with respect to their nitrogen removal performance as well as microbial community. To address this, 1724 published papers concentrating on three types of microbial aggregates, namely granules, biofilm, and flocs were compiled. A quantitative meta-analysis was carried out to compare the standard error of nitrogen removal efficiencies among these three microbial aggregates. The data sources of this meta-analysis comprised articles on granules (42%), followed by those on biofilm (33%) and flocs (25%). The granular sludge appeared to be competent in achieving the highest average nitrogen removal efficiencies of 81.1%, followed by biofilm (80.8%). Flocs provided comparatively poor removal of nitrogen pollutants with the lowest removal efficiency of 74.1%. Biofilm had the highest abundance of functional microbial communities with 43.4% on Candidatus Kuenenia and 11.2% on Candidatus Brocadia, which were detected in the anammox system as common genera. This meta-analysis suggested that the microbial aggregate types of granules and biofilm had a relatively low heterogeneity and high total nitrogen removal efficiencies for the anammox process and were the recommended microbial aggregates for anammox bacteria cultivation and operation of the anammox process.

A comparison of biofiltration performance based on bacteria and fungi for treating toluene vapors from airflow

With increasing concerns about industrial gas contaminants and the growing demand for durable and sustainable technologies, attentions have been gradually shifted to biological air pollution controls. The ability of Pseudomonas putida PTCC 1694 (bacteria) and Pleurotus ostreatus IRAN 1781C (fungus) to treat contaminated gas stream with toluene and its biological degradation was compared under similar operating conditions. For this purpose, a biofilter on the laboratory scale was designed and constructed and the tests were carried out in two stages. The first stage, bacterial testing, lasted 20 days and the second stage, fungal testing, lasted 16 days. Inlet loading rates (IL) for bacterial and fungal biofilters were 21.62 ± 6.04 and 26.24 ± 7.35 g/m³ h respectively. In general, fungal biofilter showed a higher elimination capacity (EC) than bacterial biofilter (18.1 ± 6.98 vs 13.7 ± 4.7 g/m³ h). However, the pressure drop in the fungal biofilter was higher than the bacterial biofilter (1.26 ± 0.3 vs 1 ± 0.3 mm water), which was probably due to the growth of the mycelium. Fungal biofiltration showed a better performance in the removal of toluene from the air stream.

Effects of ozone treatment on performance and microbial community composition in biofiltration systems treating ethyl acetate vapours

Ozone (O₃) treatment is an effective strategy in maintaining high efficiency and control of biomass accumulation in gas phase biofiltration. However, little is known about the long-term impact of O₃ on the microbial communities. In the present study, two biofilters treating gaseous ethyl acetate were operated continuously for 230 days with inlet loads up to 180 g m^-3∙h^-1. A biofilter operated under continuous O₃ addition (90 ppb_v) yielded consistently higher removal efficiency (RE) and elimination capacity (EC) compared to the control system. After 120 days of operation, a lower biomass content accompanied by a pH of 1.5 was observed in the ozonated biofilter, which was 2 units lower compared to the control reactor. Both reactors developed a distinct microbial community composition over the course of 230 days. The bacterial community was dominated in both biofilters by Beijerinckia and Gluconacetobacter, while Rhinocladiella similis, Trichosporon veenhuissi and Exophilia oligosperma were abundant in the fungal community. These findings suggest that ozonation of the biofiltration systems not only reduced clogging, but also contributed to the selection of biomass suitable for degradation of ethyl acetate.

Sulfur dioxide and o-xylene co-treatment in biofilter: Performance, bacterial populations and bioaerosols emissions

Sulfur dioxide (SO₂) and benzene homologs are frequently present in the off-gas during the process of sewage sludge drying. A laboratory scale biofilter was set up to co-treat SO₂ and o-xylene in the present study. SO₂ and o-xylene could be removed simultaneously in a single biofilter. Their concentration ratio in the inlet stream influenced the removal efficiencies. It is worth noting that the removal of SO₂ could be enhanced when low concentrations of o-xylene were introduced into the biofilter. Pseudomonas sp., Paenibacillus sp., and Bacillus sp. were the main functional bacteria groups in the biofilter. Sulfur-oxidizing bacteria (SOB) and o-xylene-degrading bacteria (XB) thrived in the biofilter and their counts as well as their growth rate increased with the increase in amount of SO₂ and o-xylene supplied. The microbial populations differed in counts and species due to the properties and components of the compounds being treated in the biofilter. The presence of mixed substrates enhanced the diversity of the microbial population. During the treatment process, bioaerosols including potentially pathogenic bacteria, e.g., Acinetobacter lwoffii and Aeromonas sp., were emitted from the biofilter. Further investigation is needed to focus on the potential hazards caused by the bioaerosols emitted from waste gas treatment bioreactors.

Effect of ozone injection on the long-term performance and microbial community structure of a VOCs biofilter

For biofilters treating waste gases containing volatile organic compounds (VOCs), biomass accumulation is a common problem which will induce bed clogging and significant decrease in VOCs removal efficiency during long-term operation. In this study, ozone injection was developed as a biomass control strategy, and its effects on the biofilter performance and the microbial community structure were investigated in long-term operation. Two biofilters, identified as BF1 and BF2, were operated continuously for 160 days treating gaseous toluene under the same conditions, except that 200 mg/m³ ozone was continuously injected into BF1 during days 45-160. During the operation period, ozone injection did not change the toluene removal efficiency, while the pressure drop of BF1 with ozone injection was significantly lowered compared with BF2. The wet biomass accumulation rate of BF1 was 11 g/m³/hr, which was only 46% of that in BF2. According to the carbon balance result, ozone injection also increased the toluene mineralization rate from 83% to 91%, which could be an important reason for the low biomass accumulation. The PMA-qPCR result indicated that ozone injection increased the microbial viability of the biofilm. The high-throughput sequencing result also revealed that the dominant phyla and genera were not changed significantly by ozone injection, but some ozone-tolerant genera such as Rhodanobacter, Dokdonella and Rhodococcus were enhanced by ozone exposure. All the results verified that ozone injection is capable of sustaining the long-term performance of biofilters by lowering the biomass accumulation, increasing the microbial viability and changing the microbial community structure.

Investigation of Removal Capacities of Biofilters for Airborne Viable Micro-Organisms

New emerging issues appears regarding the possible aerosolization of micro-organisms from biofilters to the ambient air. Traditional bioaerosol sampling and cultural methods used in literature offer relative efficiencies. In this study, a new method revolving around a particle counter capable of detecting total and viable particles in real time was used. This counter (BioTrak 9510-BD) uses laser-induced fluorescence (LIF) technology to determine the biological nature of the particle. The concentration of viable particles was measured on two semi-industrial pilot scale biofilters in order to estimate the Removal Efficiency in viable particles (RE_vp) in stable conditions and to examine the influence of pollutant feeding and relative humidification of the gaseous effluent on the RE_vp. The RE_vp of biofilters reached near 80% and highlighted both the stability of that removal and the statistical equivalence between two identical biofilters. Pollutant deprivation periods of 12 h, 48 h and 30 days were shown to have no influence on the biofilters’ removal capacity, demonstrating the robustness and adaptation capacities of the flora. In contrast, a 90-day famine period turned the biofilters into emitters of viable particles. Finally, the humidification of the effluent was shown to negatively influence the removal capacity for viable particles, as drying off the air was shown to increase the RE_vp from 60 to 85%.

Microbial compositions and metabolic interactions in one- and two-phase partitioning airlift bioreactors treating a complex VOC mixture

Engineered microbial ecosystems in bioscrubbers for the treatment of volatile organic compounds (VOCs) have been complicated by complex VOC mixtures from various industrial emissions. Microbial associations with VOC removal performance of the bioscrubbers are still not definitive. Here, one- and two-phase partitioning airlift bioreactors were used for the treatment of a complex VOC mixture. Microbial characteristics in both bioreactors were uncovered by high-throughput metagenomics sequencing. Results showed that dominant species with specialized VOC biodegradability were mainly responsible for high removal efficiency of relative individual VOC. Competitive enzyme inhibitions among the VOC mixture were closely related to the deterioration of removal performance for individual VOC. Relative to the mass transfer resistance, the specialized biodegrading functions of microbial inoculations and enzymatic interactions among individual VOC biodegradation also must be carefully evaluated to optimize the treatment of complex VOC mixtures in bioreactors.

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses

The human skin microbiota is quantitatively dominated by Gram-positive bacteria, detected by both culture and metagenomics. However, metagenomics revealed a huge variety of Gram-negative taxa generally considered from environmental origin. For species affiliation of bacteria in skin microbiota, clones of 16S rRNA gene and colonies growing on diverse culture media were analyzed. Species-level identification was achieved for 81% of both clones and colonies. Fifty species distributed in 26 genera were identified by culture, mostly belonging to Actinobacteria and Firmicutes, while 45 species-level operational taxonomic units distributed in 30 genera were detected by sequencing, with a high diversity of Proteobacteria. This mixed approach allowed the detection of 100% of the genera forming the known core skin Gram-negative microbiota and 43% of the known diversity of Gram-negative genera in human skin. The orphan genera represented 50% of the current skin pan-microbiota. Improved culture conditions allowed the isolation of Roseomonas mucosa, Aurantimonas altamirensis and Agrobacterium tumefaciens strains from healthy skin. For proteobacterial species previously described in the environment, we proposed the existence of skin-specific ecotypes, which might play a role in the fine-tuning of skin homeostasis and opportunistic infections but also act as a shuttle between environmental and human microbial communities. Therefore, skin-associated proteobacteria deserve to be considered in the One-Health concept connecting human health to the health of animals and the environment.

Management of Microbial Communities through Transient Disturbances Enhances the Functional Resilience of Nitrifying Gas-Biofilters to Future Disturbances

Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.

Succession of microorganisms in a plate-type air treatment biofilter during filtration of various volatile compounds

Changes in the number and species diversity of cultivable microorganisms in a newly developed plate-type biofilter during filtration of various volatile pollutants were studied. The novelty of the investigation is the monitoring of microorganism succession in different parts of biofilter plates with original packing material consisting of birch fibre and needle-punched non-woven fabric. It was shown that the largest number of fungi and yeasts develop on the top and middle, while bacteria develop on the bottom and middle parts of plates. The number of microorganisms depends on the origin of the pollutant, the pH and temperature inside the biofilter and the moisture of the porous plates. The statistically significant correlation between the number of microorganisms and inlet concentration of acetone was estimated, while ammonia showed a negative influence on yeast distribution. Paecilomyces variotii, Rhodotorula mucilaginosa and Bacillus subtilis were the most common organisms found during filtration of all examined volatiles; however, some differences of microbial communities in different parts of the biofilter plates and filtrated volatile compounds were obtained.

Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing

Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

Spatial heterogeneity in degradation characteristics and microbial community composition of pesticide biopurification systems

AIMS

To investigate spatial and temporal differences in degradation characteristics and microbial community composition of pesticide biopurification systems.

METHODS AND RESULTS

Pilot-scale biofilters were supplemented with the potato-sprouting suppressant chloropropham. Two biofilters were inoculated with a chloropropham-degrading mixed culture, while the other two were not inoculated. Biodegradation rate, size and composition of the microbial community were monitored during 72 days at different biofilter depths. First of all, results showed that inoculation was not necessary to obtain efficient degradation although it shortens the biofilter's start-up period. Secondly, a higher biodegradation rate and chloropropham- and 3-chloroaniline-degrading microbial community size could be seen in the top part of the inoculated as well as the noninoculated biofilters. Finally, analysis of the microbial community composition shows that no clear spatial stratification of the microbial community could be found in any biofilter. However, the microbial diversity increases over time in all biofilters and on all biofilter depths, suggesting that during the time of the experiment, the biofilters develop a broad carrying capacity in which a genetically very diverse range of chloropropham- and 3-chloroaniline-degrading species can thrive.

CONCLUSIONS

In this study, a vertical gradient of the chloropropham- and 3-chloroaniline-degrading community composition, in terms of density and temporal and spatial diversity, was clearly established and was directly connected to a vertical gradient of chloropropham biodegradation activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The major part of degradation activity takes place in the top part of the biofilter, suggesting that it could be possible to use shorter biofilter reactors or higher loading rates to treat chloropropham waste streams, making this type of bioremediation technique economically more feasible.

Massilia umbonata sp. nov., able to accumulate poly-β-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm

A bacterial strain, designated strain LP01(T), was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain-negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472(T) and M. lutea DSM 17473(T). DNA-DNA hybridization showed low relatedness of strain LP01(T) to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia. The DNA G+C content was 66.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study suggest that strain LP01(T) represents a novel species of the genus Massilia, for which the name Massilia umbonata sp. nov. is proposed. The type strain is LP01(T) ( = CECT 7753(T) = DSM 26121(T)).

Microbial community analysis in biotrickling filters treating isopropanol air emissions

The evolution of the microbial community was analysed over one year in two biotrickling filters operating under intermittent feeding conditions and treating isopropanol emissions, a pollutant typically found in the flexography sector. Each reactor was packed with one media: plastic cross-flow-structured material or polypropylene rings. The communities were monitored by fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA region. After inoculation with activated sludge, the biotrickling filters were operated using inlet loads (ILs) from 20 to 65 g C m(-3) h(-1) and empty-bed residence times (EBRTs) from 14 to 160 s. Removal efficiencies higher than 80% were obtained with ILs up to 35 g C m(-3) h(-1) working at EBRTs as low as 24 s. There was an increase in the total percentage of the target domains of up to around 80% at the end of the experiment. Specifically, the Gammaproteobacteria domain group, which includes the well-known volatile organic compound (VOC)-degrading species such as Pseudomonas putida, showed a noticeable rise in the two biotrickling filters of 26% and 27%, respectively. DGGE pattern band analysis revealed a stable band of Pseudomonas putida in all the samples monitored, even in the lower diversity communities. In addition, at similar operational conditions, the biotrickling filter with a greater relative abundance of Pseudomonas sp. (19.2% vs. 8%) showed higher removal efficiency (90% vs. 79%). Results indicate the importance of undertaking a further in-depth study of the involved species in the biofiltration process and their specific function.

One-stage biotrickling filter for the removal of a mixture of volatile pollutants from air: performance and microbial community analysis

The biodegradation of gas-phase mixtures of methanol, α-pinene and H2S was examined in a biotrickling filter (BTF), inoculated with a microbial consortium composed of an autotrophic H2S-degrading culture, and pure strains of Candida boidinii, Rhodococcus erythropolis, and Ophiostoma stenoceras. The inlet concentrations of methanol, α-pinene and H2S varied from 0.05 to 3.3 gm(-3), 0.05 to 2.7 gm(-3), and 0.01 to 1.4 gm(-3), respectively, at empty bed residence times (EBRT) of either 38 or 26s. The maximum elimination capacities (ECmax) of the BTF were 302, 175, and 191 gm(-3)h(-1), with 100%, 67%, and >99% removal of methanol, α-pinene and H2S, respectively. The presence of methanol showed an antagonistic removal pattern for α-pinene, but the opposite did not occur. For α-pinene, inlet loading rates (ILRs) >150 gα-pinenem(-3)h(-1) affected its own removal in the BTF. The presence of H2S did not show any declining effect on the removal of both methanol and α-pinene.

A comparative study of fungal and bacterial biofiltration treating a VOC mixture

Bacterial biofilters usually exhibit a high microbial diversity and robustness, while fungal biofilters have been claimed to better withstand low moisture contents and pH values, and to be more efficient coping with hydrophobic volatile organic compounds (VOCs). However, there are only few systematic evaluations of both biofiltration technologies. The present study compared fungal and bacterial biofiltration for the treatment of a VOC mixture (propanal, methyl isobutyl ketone-MIBK, toluene and hexanol) under the same operating conditions. Overall, fungal biofiltration supported lower elimination capacities than its bacterial counterpart (27.7 ± 8.9 vs 40.2 ± 5.4 gCm(-3) reactor h(-1)), which exhibited a final pressure drop 60% higher than that of the bacterial biofilter due to mycelial growth. The VOC mineralization ratio was also higher in the bacterial bed (≈ 63% vs ≈ 43%). However, the substrate biodegradation preference order was similar for both biofilters (propanal>hexanol>MIBK>toluene) with propanal partially inhibiting the consumption of the rest of the VOCs. Both systems supported an excellent robustness versus 24h VOC starvation episodes. The implementation of a fungal/bacterial coupled system did not significantly improve the VOC removal performance compared to the individual biofilter performances.

Multiplex and quantitative pathogen detection with high-resolution capillary electrophoresis-based single-strand conformation polymorphism

Among the molecular diagnostic methods for bacteria-induced diseases, capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) combined with 16S rRNA gene-specific PCR has enormous potential because it can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S rRNA gene-specific markers into separate peaks. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this report, a protocol for the detection of 12 pathogenic bacteria is provided. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing the easy identification of the pathogens.

Resistance and resilience of removal efficiency and bacterial community structure of gas biofilters exposed to repeated shock loads

Since full-scale biofilters are often operated under fluctuating conditions, it is critical to understand their response to transient states. Four pilot-scale biofilters treating a composting gas mixture and undergoing repeated substrate pulses of increasing intensity were studied. A systematic approach was proposed to quantify the resistance and resilience capacity of their removal efficiency, which enabled to distinguish between recalcitrant (ammonia, DMDS, ketones) and easily degradable (esters and aldehyde) compounds. The threshold of disturbing shock intensity and the influence of disturbance history depended on the contaminant considered. The spatial and temporal distribution of the bacterial community structure in response to the perturbation regime was analysed by Denaturing Gradient Gel Electrophoresis (DGGE). Even if the substrate-pulses acted as a driving force for some community characteristics (community stratification), the structure-function relationships were trickier to evidence: the distributions of resistance and composition were only partially coupled, with contradictory results depending on the contaminant considered.

Bacterial dynamics in steady-state biofilters: beyond functional stability

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

Diversity of bacterial communities that colonize the filter units used for controlling plant pathogens in soilless cultures

In recent years, increasing the level of suppressiveness by the addition of antagonistic bacteria in slow filters has become a promising strategy to control plant pathogens in the recycled solutions used in soilless cultures. However, knowledge about the microflora that colonize the filtering columns is still limited. In order to get information on this issue, the present study was carried out over a 4-year period and includes filters inoculated or not with suppressive bacteria at the start of the filtering process (two or three filters were used each year). After 9 months of filtration, polymerase chain reaction (PCR)-single strand conformation polymorphism analyses point out that, for the same year of experiment, the bacterial communities from control filters were relatively similar but that they were significantly different between the bacteria-amended and control filters. To characterize the changes in bacterial communities within the filters, this microflora was studied by quantitative PCR, community-level physiological profiles, and sequencing 16SrRNA clone libraries (filters used in year 1). Quantitative PCR evidenced a denser bacterial colonization of the P-filter (amended with Pseudomonas putida strains) than control and B-filter (amended with Bacillus cereus strains). Functional analysis focused on the cultivable bacterial communities pointed out that bacteria from the control filter metabolized more carbohydrates than those from the amended filters whose trophic behaviors were more targeted towards carboxylic acids and amino acids. The bacterial communities in P- and B-filters both exhibited significantly more phylotype diversity and markedly distinct phylogenetic compositions than those in the C-filter. Although there were far fewer Proteobacteria in B- and P-filters than in the C-filter (22% and 22% rather than 69% of sequences, respectively), the percentages of Firmicutes was much higher (44% and 55% against 9%, respectively). Many Pseudomonas species were also found in the bacterial communities of the control filter. The persistence of the amended suppressive-bacteria in the filters is discussed with regards to the management of suppressive microflora in soilless culture.

Butyric acid- and dimethyl disulfide-assimilating microorganisms in a biofilter treating air emissions from a livestock facility

Biofiltration has proven an efficient tool for the elimination of volatile organic compounds (VOCs) and ammonia from livestock facilities, thereby reducing nuisance odors and ammonia emissions to the local environment. The active microbial communities comprising these filter biofilms have not been well characterized. In this study, a trickle biofilter treating air from a pig facility was investigated and proved efficient in removing carboxylic acids (>70% reduction), mainly attributed to the primary filter section within which reduced organic sulfur compounds were also depleted (up to 50%). The secondary filter eliminated several aromatic compounds: phenol (81%), p-cresol (89%), 4-ethylphenol (68%), indole (48%), and skatole (69%). The active butyric acid degrading bacterial community of an air filter sample was identified by DNA stable-isotope probing (DNA-SIP) and microautoradiography, combined with fluorescence in situ hybridization (MAR-FISH). The predominant 16S rRNA gene sequences from a clone library derived from "heavy" DNA from [(13)C(4)]butyric acid incubations were Microbacterium, Gordonia, Dietzia, Rhodococcus, Propionibacterium, and Janibacter, all from the Actinobacteria. Actinobacteria were confirmed and quantified by MAR-FISH as being the major bacterial phylum assimilating butyric acid along with several Burkholderiales-related Betaproteobacteria. The active bacterial community assimilating dimethyl disulfide (DMDS) was characterized by DNA-SIP and MAR-FISH and found to be associated with the Actinobacteria, along with a few representatives of Flavobacteria and Sphingobacteria. Interestingly, ammonia-oxidizing Betaproteobacteria were also implicated in DMDS degradation, as were fungi. Thus, multiple isotope-based methods provided complementary data, enabling high-resolution identification and quantitative assessments of odor-eliminating Actinobacteria-dominated populations of these biofilter environments.

Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration

Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.

Simultaneous quantitative detection of 12 pathogens using high-resolution CE-SSCP

Several methods based on screening for a 16S ribosomal RNA gene marker have been developed for rapid and sensitive detection of pathogenic microorganisms. One such method, CE-based SSCP (CE-SSCP), has enormous potential because the technique can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S ribosomal RNA gene-specific markers unless combined with additional modification steps. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this study, we developed a method based on a high-resolution CE-SSCP system using a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer that is capable of simultaneous and quantitative detection of 12 clinically important pathogens. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing easy identification of pathogens. A series of experiments using different amounts of genomic pathogen DNA showed that the method had a limit of detection of 0.31-1.56 pg and a dynamic range of approximately 10(2). These results indicate that high-resolution CE-SSCP systems have considerable potential in the clinical diagnosis of bacteria-induced diseases.

Effect of nitrogen source on methanol oxidation and genetic diversity of methylotrophic mixed cultures enriched from pulp and paper mill biofilms

Methanol-oxidizing bacteria may play an important role in the development and use of biological treatment systems for the removal of methanol from industrial effluents. Optimization of methanol degradation potential in such systems is contingent on availability of nutrients, such as nitrogen, in the most favorable form and concentration. To that end, this study examined the variation in growth, methanol degradation, and bacterial diversity of two mixed methylotrophic cultures that were provided nitrogen either as ammonium or nitrate and in three different concentrations. Methanol-degrading cultures were enriched from biofilms sampled at a pulp and paper mill and grown in liquid batch culture with methanol as the only carbon source and either ammonium or nitrate as the only added nitrogen source. Results indicate that growth and methanol removal of the mixed cultures increase directly with increased nitrogen, added in either form. However, methanol removal and bacterial diversity, as observed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods, were higher when using nitrate as the nitrogen source for enrichment and growth, rather than ammonium. Based on results described here, nitrate may potentially be a better nitrogen source when enriching or working with mixed methylotrophic cultures, and possibly more effective when used as a nutrient addition to biofilters.

Triblock copolymer matrix-based capillary electrophoretic microdevice for high-resolution multiplex pathogen detection

Rapid and simple analysis for the multiple target pathogens is critical for patient management. CE-SSCP analysis on a microchip provides high speed, high sensitivity, and a portable genetic analysis platform in molecular diagnostic fields. The capability of separating ssDNA molecules in a capillary electrophoretic microchannel with high resolution is a critical issue to perform the precise interpretation in the electropherogram. In this study, we explored the potential of poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) (PEO-PPO-PEO) triblock copolymer as a sieving matrix for CE-SSCP analysis on a microdevice. To demonstrate the superior resolving power of PEO-PPO-PEO copolymers, 255-bp PCR amplicons obtained from 16S ribosomal RNA genes of four bacterial species, namely Proteus mirabilis, Haemophilus ducreyi, Pseudomonas aeruginosa, and Neisseria meningitidis, were analyzed in the PEO-PPO-PEO matrix in comparison with 5% linear polyacrylamide and commercial GeneScan gel. Due to enhanced dynamic coating and sieving ability, PEO-PPO-PEO copolymer displayed fourfold enhancement of resolving power in the CE-SSCP to separate same-sized DNA molecules. Fivefold input of genomic DNA of P. aeruginosa and/or N. meningitidis produced proportionally increased corresponding amplicon peaks, enabling correct quantitative analysis in the pathogen detection. Besides the high-resolution sieving capability, a facile loading and replenishment of gel in the microchannel due to thermally reversible gelation property makes PEO-PPO-PEO triblock copolymer an excellent matrix in the CE-SSCP analysis on the microdevice.

Methanol removal efficiency and bacterial diversity of an activated carbon biofilter

Motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. This system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. The biofilter system, composed of a novel packing mixture, provided an excellent support for growth and activity of methanol-degrading bacteria, resulting in approximately 100% methanol removal efficiency for loading rates of 1-17 g/m(3) packing/h, when operated both with and without inoculum containing enriched methanol-degrading bacteria. Although bacterial diversity and abundance varied over the length of the biofilter, the populations present rapidly formed a stable community that was maintained over the entire 138-day operation of the system and through variable operating conditions, as observed by PCR-DGGE methods that targeted all bacteria as well as specific methanol-oxidizing microorganisms. Phylogenetic analysis of bands excised and sequenced from DGGE gels indicated that the biofilter system supported a diverse community of methanol-degrading bacteria, with high similarity to species in the genera Methylophilus (beta-proteobacteria), Hyphomicrobium and Methylocella (both alpha-proteobacteria).

Parallel analysis of antimicrobial activities in microbial community by SSCP based on CE

Conventional antimicrobial activity analyses such as the broth dilution method and disk diffusion test are considerably demanding processes for new antimicrobial agent discovery and sensitive diagnosis of infectious diseases. Here, we developed a new antimicrobial activity analysis system using CE-based SSCP (CE-SSCP) combined with 16S rRNA gene-specific PCR (PCR/CE-SSCP). Using this method, the population change in the microbial community in response to specific antimicrobial agents could be quantified with a high sensitivity and accuracy from a small sample amount. Using a mixture of microorganisms comprising Escherichia coli, Corynebacterium glutamicum, Acinetobacter calcoaceticus, and Staphylococcus aureus as a model system, the linear correlation between the genomic DNA concentrations and peak areas in 16S rRNA gene-specific PCR/CE-SSCP was determined; consequently, quantification of cell concentrations could be demonstrated using this method. Compared to the minimum inhibitory concentration (MIC) values from the conventional broth dilution method, this new system provided almost the same MIC values for popular antimicrobial agents such as kanamycin, spectinomycin, and streptomycin. The results demonstrated that the newly developed method can be a substitute for the conventional antimicrobial analysis method and highlighted its high potential in the areas of new antimicrobial agent discovery and clinical diagnosis.

Long-term performance of peat biofilters treating ethyl acetate, toluene, and its mixture in air

Three laboratory-scale peat biofilters were operated at 90 s empty bed residence time (EBRT) for over a year. Biodegradation of ethyl acetate, toluene, or a 1:1 mixture were investigated. In first stage, inlet concentration was progressively increased from 0.4 to 4.5 g/m(3). The maximum elimination capacity (EC) found for ethyl acetate was 190 gC/m(3).h, and it was not affected by toluene. The maximum EC found for toluene as a sole contaminant was 150 gC/m(3).h, but the presence of ethyl acetate decreased the toluene maximum EC to 80 gC/m(3).h. From respirometry monitoring, values of 3.19 g CO(2)/gC and 3.06 g CO(2)/gC for pure ethyl acetate and pure toluene, respectively, were found, with overall yield coefficients of 0.13 g dry biomass produced per gram ethyl acetate consumed and 0.28 g dry biomass produced per gram toluene consumed. CO(2) production in the 1:1 mixture was successfully simulated. Dynamics of living and dead cells were monitored in four sections of the biofilters. Concentrations ranged between 2.6 x 10(9) and 3.0 x 10(10) cells per gram-dry peat for total bacteria, and 2.4 x 10(9)-1.9 x 10(10) cells per gram-dry peat for living bacteria. At high loads loss of bacterial density in the inlet zones, and increase in the dead cells percentages up to 60% was observed. In second stage, long-term performance at an inlet concentration of 1.5 g/m(3) was evaluated to show the process feasibility. Good agreement with previous data was obtained in terms of EC and CO(2) production. Restoration of living cells proportion was also observed.

Performance and microbial analysis of defined and non-defined inocula for the removal of dimethyl sulfide in a biotrickling filter

The performance and microbial communities of three differently inoculated biotrickling filters removing dimethyl sulfide (DMS) were compared. The biotrickling filters were inoculated with Thiobacillus thioparus TK-m (THIO), sludge (HANDS) and sludge + T. thioparus TK-m + Hyphomicrobium VS (HANDS++), respectively. The criteria investigated were length of the start-up period, the maximum elimination capacity, and the effects of intermittent loading rates, low pH, peak loading and very low loading rate on the DMS removal efficiency. The HANDS++ reactor exhibited the best performance considering all treatments. HANDS performed almost equally well as HANDS++, except during the determination of the EC(max), while THIO was generally the least efficient. During stable DMS loading at concentrations of 20 ppmv or lower, all reactors exhibited similar and high removal efficiencies (>99%). Denaturing gradient gel electrophoresis (DGGE) analysis showed the establishment of T. thioparus in the biofilm of all reactors, but not of Hyphomicrobium VS. Quantitative monitoring of the introduced bacterial strains was performed with a newly developed real-time PCR protocol. Initially, the inoculated strains were exclusively found in the reactors in which they were added. Afterwards, however, both strains developed in the biofilm of all three reactors, although T. thioparus attained higher cell densities than Hyphomicrobium. The presence of T. thioparus in THIO was related with the DMS loading rates that were applied, in the sense that intermittent DMS loading and very low DMS loading rates (0.5 ppmv) induced a decrease in gene copy numbers. Real-time PCR and DGGE both gave consistent results regarding the presence of Hyphomicrobium VS and Thiobacillus thioparus TK-m in the reactors. Only real-time PCR could be used to detect bacteria comprising of less than 1.4% of the total bacterial community ( approximately 10(5) copies ring(-1)).